Merge branch 'photonTest' into 'develop'

photon Test

See merge request e040/e0404/pyRadPlan!180

Author: wahln

README.md

@@ -53,7 +53,13 @@ A minimal script is very similar to matRad's example [`matRad.m`](https://github
 ```python
 from importlib import resources
 import pymatreader
-from pyRadPlan import load_patient, IonPlan, generate_stf, calc_dose_influence, fluence_optimization
+from pyRadPlan import (
+    load_patient,
+    IonPlan,
+    generate_stf,
+    calc_dose_influence,
+    fluence_optimization,
+)
 
 #  Read patient from provided TG119.mat file and validate data
 tg119_path = resources.files("pyRadPlan.data.phantoms").joinpath("TG119.mat")
@@ -93,6 +99,7 @@ Instead of using above top-level workflow functions and a central plan configura
 ```python
 ...
 from pyRadPlan.stf import StfGeneratorIMPT
+
 # Create a plan object
 pln = IonPlan(radiation_mode="protons", machine="Generic")
 
@@ -104,7 +111,7 @@ pln = IonPlan(radiation_mode="protons", machine="Generic")
 stf_gen = StfGeneratorIMPT()
 stf_gen.gantry_angles = [90, 270]
 stf_gen.couch_angles = [0, 0]
-stf = stf_gen.generate(ct,cst)
+stf = stf_gen.generate(ct, cst)
 ```
 
 If you are interested in helping with development, get in touch, read the contributing guidelines, and the developer note below.

test/dose/test_hongpb.py

@@ -22,7 +22,7 @@ def test_protons_cd_forward(test_data_protons):
     result_py = calc_dose_forward(ct, cst, stf, pln, weights=None)
     result_py = sitk.GetArrayFromImage(result_py["physical_dose"])
 
-    result_matRad_rot = np.swapaxes(result["physicalDose"], 0, 1)
+    result_matRad_rot = np.transpose(result["physicalDose"], (2, 0, 1))
     # only comparing to 1e-4 since matRad rounds to 4 digits
     assert np.allclose(result_py, result_matRad_rot, atol=1e-4)
 
@@ -44,7 +44,7 @@ def test_helium_cd_forward(test_data_helium):
     result_py = calc_dose_forward(ct, cst, stf, pln, weights=None)
     result_py = sitk.GetArrayFromImage(result_py["physical_dose"])
 
-    result_matRad_rot = np.swapaxes(result["physicalDose"], 0, 1)
+    result_matRad_rot = np.transpose(result["physicalDose"], (2, 0, 1))
     # only comparing to 1e-4 since matRad rounds to 4 digits
     assert np.allclose(result_py, result_matRad_rot, atol=1e-4)
 
@@ -55,7 +55,7 @@ def test_carbon_cd_forward(test_data_carbon):
     result_py = calc_dose_forward(ct, cst, stf, pln)
     result_py = sitk.GetArrayFromImage(result_py["physical_dose"])
 
-    result_matRad_rot = np.swapaxes(result["physicalDose"], 0, 1)
+    result_matRad_rot = np.transpose(result["physicalDose"], (2, 0, 1))
     # only comparing to 1e-4 since matRad rounds to 4 digits
     assert np.allclose(result_py, result_matRad_rot, atol=1e-4)
 
@@ -66,7 +66,7 @@ def test_oxygen_cd_forward(test_data_oxygen):
     result_py = calc_dose_forward(ct, cst, stf, pln)
     result_py = sitk.GetArrayFromImage(result_py["physical_dose"])
 
-    result_matRad_rot = np.swapaxes(result["physicalDose"], 0, 1)
+    result_matRad_rot = np.transpose(result["physicalDose"], (2, 0, 1))
     # only comparing to 1e-4 since matRad rounds to 4 digits
     assert np.allclose(result_py, result_matRad_rot, atol=1e-4)
 

test/dose/test_svdpb.py

@@ -2,6 +2,7 @@
 import numpy as np
 
 from pyRadPlan.dose import calc_dose_forward
+from pyRadPlan.visualization._plot_slice import plot_slice
 
 
 # TODO: PhotonEngine does not yet have sub-sampling.
@@ -14,10 +15,9 @@ def test_photons(test_data_photons):
 
     result_py = calc_dose_forward(ct, cst, stf, pln, weights=None)
     result_py = sitk.GetArrayFromImage(result_py["physical_dose"])
+    result_matRad = np.transpose(result["physicalDose"], (2, 0, 1))
 
-    result_matRad_rot = np.swapaxes(result["physicalDose"], 0, 1)
-
-    # assert np.allclose(result_py, result_matRad_rot, atol=1e-4)
+    assert np.allclose(result_py, result_matRad, atol=1e-2)
 
     # Keeping this for debugging:
     # plot_slice(